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The Seal (Logo) of the Aga Khan University is a visual representation of the principles which underlie the founding of the University.

The circular form of the Seal, with its different levels of imagery contained in concentric circles, has its visual roots in the rosettes of early Islamic periods.

The circle also symbolizes the world and reflects the internationality of the Aga Khan University. At the centre of the Seal is a star, or sun. Light is a universal symbol for the enlightenment that education provides. The light emanating from the star is also symbolic of Nur (Divine light).

The star incorporates 49 points to commemorate the University's founding by His
Highness Prince Karim Aga Khan, the Forty-Ninth Imam of the Ismaili Muslims.
The outer ring circumscribes a Quranic Ayat (3:103) rendered in classic thuluth script and reads as follows:

And hold fast,
All together, by the rope
Which God (stretches out for you),
And be not divided among yourselves,
And remember with gratitude
God's favour on you:
For ye were enemies
And He joined your hearts
In love, so that by His grace
Ye became brethren